Infectious diseases kill many people worldwide each year. One reason that infectious diseases claim so many lives is that pathogens are all around us. We can be infected by harmful microorganisms, such as bacteria, viruses, and fungi, in myriad ways. For example, we ingest them from food and water sources, touch and breathe them in physical environments, including homes, workplaces, places of commerce, and recreational settings, and get exposed to them through contact with other infected individuals.
Unfortunately, detecting a pathogen is difficult because the relevant sample typically includes a large amount of irrelevant material, such as nucleic acids from the host or patient. Irrelevant material interferes with the ability to do PCR or probe hybridization, sometime making detection impossible. Moreover, existing detection methods are limited in the ability to detect large DNA fragments. PCR can introduce errors and fails to capture information about epigenetic modifications such as methylation and may introduce errors in the sequence. In addition, both capture- and amplification-based methods lack the sensitivity to detect targets when the ratio of target-to-background is very low. Finally, the ability to multiplex is limited, making it difficult to detect more than one pathogen in a sample.